NCBI Ixodes scapularis Annotation Release 103

The RefSeq genome records for Ixodes scapularis were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.


Annotation Release information

This annotation should be referred to as NCBI Ixodes scapularis Annotation Release 103

Annotation release ID: 103
Date of Entrez queries for transcripts and proteins: Jul 1 2021
Date of submission of annotation to the public databases: Jul 7 2021
Software version: 9.0

Assemblies

The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
ASM1692078v2GCF_016920785.2University of Maryland06-23-2021Referenceunplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

FeatureASM1692078v2
Genes and pseudogenes help38,656
  protein-coding26,659
  non-coding5,760
  Transcribed pseudogenes17
  Non-transcribed pseudogenes6,220
  genes with variants4,204
  Immunoglobulin/T-cell receptor gene segments0
  other0
mRNAs34,235
  fully-supported24,474
  with > 5% ab initio help6,830
  partial1,349
  with filled gap(s) help177
  known RefSeq (NM_) help0
  model RefSeq (XM_)34,235
non-coding RNAs help7,071
  fully-supported3,702
  with > 5% ab initio help0
  partial7
  with filled gap(s) help2
  known RefSeq (NR_) help0
  model RefSeq (XR_) help4,324
pseudo transcripts help19
  fully-supported18
  with > 5% ab initio help0
  partial0
  with filled gap(s) help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help19
CDSs34,235
  fully-supported24,474
  with > 5% ab initio help7,206
  partial1,337
  with major correction(s) help439
  known RefSeq (NP_) help0
  model RefSeq (XP_) help34,235

Detailed reports

The counts below do not include pseudogenes.

BUSCO analysis of gene annotation

BUSCO v4.1.4 (Simão et al 2015, PMID: 26059717) was run in "protein" mode on the annotated gene set picking one longest protein per gene, and run using the arachnida_odb10 lineage dataset. Results are reported for the gene set from the primary assembly unit, and presented in BUSCO notation (C:complete [S:single-copy, D:duplicated], F:fragmented, M:missing, n:number of genes used).

Alignment of the annotated proteins to a set of high-quality proteins

The final set of annotated proteins was searched with BLASTP against the UniProtKB/Swiss-Prot curated proteins, using the annotated proteins as the query and the high-quality proteins as the target. Out of 26659 coding genes, 15328 genes had a protein with an alignment covering 50% or more of the query and 3214 had an alignment covering 95% or more of the query.

Definition of query and target coverage. The query coverage is the percentage of the annotated protein length that is included in the alignment. The target coverage is the percentage of the target length that is included in the alignment.

Below is a cumulative graph displaying the number of genes with alignments above a given query or target coverage threshold. For comparison, corresponding statistics for other organisms annotated by the NCBI eukaryotic annotation pipeline were added to the graph.

Query: annotated proteins
Target: UniProtKB/Swiss-Prot curated proteins

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker (if calculated), for each assembly. RepeatMasker results are only calculated for organisms with complete Dfam HMM model collections.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker and RepeatMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker
ASM1692078v2GCF_016920785.263.83%42.13%

Transcript and protein alignments

The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign, minimap2, or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Transcript alignments

RNA-Seq alignments

The following RNA-Seq reads from the Sequence Read Archive were also used for gene prediction:

  Hide alignments statistics, by sample (SAME, SAMN, SAMD, DRS)
  Show alignments statistics, by run (ERR, SRR, DRR)

SRA Long Read Alignment Statistics

The following long read RNA-Seq reads (PacBio, Oxford Nanopore, 454, or other long-read sequencing technologies) from the Sequence Read Archive were also used for gene prediction:

Protein alignments

Assembly-assembly alignments of current to previous assembly

When the assembly changes between two rounds of annotation, genes in the current and the previous annotation are mapped to each other using the genomic alignments of the current assembly to the previous assembly so that gene identifiers can be preserved. The success of the remapping depends largely on how well the two assembly versions align to each other.

Below are the percent coverage of one assembly by the other and the average percent identity of the alignments. The 'First pass' alignments are reciprocal best hits, while the 'Total' alignments also include 'Second pass' or non-reciprocal best alignments. For more information about the assembly-assembly alignment process, please visit the NCBI Genome Remapping Service page.

First PassTotal
JADPSH02 (Current) Coverage: 90.03%JADPSH02 (Current) Coverage: 94.33%
Ixodes_scapularus_ComboLowHiFi (Previous) Coverage: 87.31%Ixodes_scapularus_ComboLowHiFi (Previous) Coverage: 93.30%
Percent Identity: 99.31%Percent Identity: 98.91%

Comparison of the current and previous annotations

The annotation produced for this release (103) was compared to the annotation in the previous release (102) for each assembly annotated in both releases. Scores for current and previous gene and transcript features were calculated based on overlap in exon sequence and matches in exon boundaries. Pairs of current and previous features were categorized based on these scores, whether they are reciprocal best matches, and changes in attributes (gene biotype, completeness, etc.). If the assembly was updated between the two releases, alignments between the current and the previous assembly were used to match the current and previous gene and transcript features in mapped regions.

The table below summarizes the changes in the gene set for each assembly as a percent of the number of genes in the current annotation release, and provides links to the details of the comparison in tabular format and in a Genome Workbench project.

ASM1692078v2 (Current) to Ixodes_scapularus_ComboLowHiFi (Previous)
Identical help38%
Minor changes help34%
Major changes help14%
New help14%
Deprecated help20%
Other help<1%
Download the reporttabular, Genome Workbench

References

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